It is my understanding that the Search Policy only applies to Policy Packages. Is this correct?

We've been seeing some strange problems with ZEN applications and I was wondering if it had something to do with our Search Policies.

The problem we have been having:

Running ZDM 6.5 SP1. The agents are I created an application object and associated it to our "users" container. Some people can see the object, others cannot, even though both are in the same "users" container. If I specifically associate the application object to those who cannot see it, it suddenly shows up.

Any ideas?